Mitochondria analytics
Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume
visualize all mitochondria in a cell of interest
Contents
Folders
classifier
folder: mitochondria classifier using random forests for pyramidal
neurons in the Layer 2/3 volume.
mito_to_mito_distance_statistics
folder: summary statistics for mitochondria-to-mitochondria (mito
centroid-to-mito centroid) used in the classifier analysis.
node_metrics
folder: derivation of mitochondria segmentation node metrics
(“nodeplots”).
Visualization tools
Visualize a single mitochondrion of interest in Neuroglancer
neuroglancer_link_generator_mitochondria_visualization_version.ipynb:
generate a Neuroglancer link for a single cellid and single
mitochondrion from the
pni_mito_cellswskel_v185_fullstats.csv datatable. The view
will be centered at the centroid of the mitochondrion in the volume.
neuroglancer link to a single mitochondrion with crosshair at the mito centroid
Visualize all mitochondria in a neuron of interest in Neuroglancer
neuroglancer_link_generator_all_mitochondria.ipynb:
generate a Neuroglancer link for all the mitochondria in a single cellid
of interest pulling the mito ids from the
211019_mitochondria_info.csv datatable.
neuroglancer link generator for all mitochondria in a cell
Visualize neuronal mitochondria by compartment in Neuroglancer
neuroglancer_link_generator_neuronalmitochondria_bycompartment.ipynb:
as above, but allows to select for a compartment of interest. Neuronal
compartment assignments are based on the method described by
Reconstruction of neocortex: Organelles, compartments, cells,
circuits, and activity Turner
et al, Cell 2022.
neuroglancer link generator for mitochondria by compartment
3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer.ipynb:
generate a 3D interactive view of all mitochondria in a cell of
interest. Note this method has significant file download and space
requirements compared to using the Neuroglancer viewer.
3D visualizer of all mitochondria in a cell
3D visualizer of all mitochondria and synapses in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer_with_synapses.ipynb:
generate a 3D interactive view of all mitochondria in a cell of interest
along with the pre- and post-syanptic sites. Note this method has
significant file download and space requirements compared to using the
Neuroglancer viewer.
3D visualizer of all mitochondria and synapses in a cell
3D vector plots by cellid lookup by neuronal subtype
mitochondria_3d_vector_plots_by_cellid_lookup_by_neuronal_subtype.ipynb:
generate 3D interactive scatterplots in Plotly, 3D quiver plots in
matplotlib, and a Neuroglancer views with this notebook. Uses a
dataframe that generates spatial and vector calculations from the
original mitochondria dataframe by Turner et al. Download
mito_above_soma.csv in the data
folder.
3D quiver plot of mito centroid with bounding box distance vector
3D visualization for mitochondria within a 45 degree cone above soma
3dvisualizer_for_withincone.ipynb:
generate 3D interactive scatterplots in Plotly, 3D quiver plots in
matplotlib, and Neuroglancer views with this notebook. Uses a dataframe
that generates spatial, vector, and cone angle calculations from the
original mitochondria dataframe by Turner et al. Download
pyr_all.csv in the data
folder. Special thanks to Qiao Liu and Wanwen Zeng at Stanford for
their assistance in debugging the code.
3D scatterplot using Plotly for visualizing mitochondria within a 45 degree cone above soma
Nodeplot for mitochondria segmentation node metrics
Example nodeplot (nodeid vs. nodedist by compartment color) for
pyramidal neuron cellid 648518346349537297. This example shows that
certain mitochondria where the compartment is unidentified could
potentially be inferred from the mitochondria node metrics data. See
also node_metrics
folder for additional details.
matplotlib scatterplot of nodeid vs. nodedist by compartment color from mitochondria segmentation node metrics